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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 145 records · Page 8Linked to original sources
bioRxiv2020

Chromosome-autonomous feedback downregulates meiotic DSB competence upon synaptonemal complex formation

The number of DNA double-strand breaks (DSBs) initiating meiotic recombination is elevated in Saccharomyces cerevisiae mutants that are globally defective in forming crossovers and synaptonemal complex (SC), a protein scaffold juxtaposing homologous chromosomes. These mutants thus appear to lack a negative feedback loop that inhibits DSB formation when homologs engage one another. This feedback is predicted to be chromosome autonomous, but this has not been tested. Moreover, what chromosomal process is recognized as "homolog engagement" remains unclear. To address these questions, we evaluated effects of homolog engagement defects restricted to small portions of the genome using karyotypically abnormal yeast strains with a homeologous chromosome V pair, monosomic V, or trisomy XV. We found that homolog-engagement-defective chromosomes incurred more DSBs, concomitant with prolonged retention of the DSB-promoting protein Rec114, while the rest of the genome remained unaffected. SC-deficient, crossover-proficient mutants ecm11 and gmc2 experienced increased DSB numbers diagnostic of homolog engagement defects. These findings support the hypothesis that SC formation provokes DSB protein dissociation, leading in turn to loss of a DSB competent state. Our findings show that DSB number is regulated in a chromosome-autonomous fashion and provide insight into how homeostatic DSB controls respond to aneuploidy during meiosis. bioRxiv version 2 (September 2020) We added one bioRxiv citation in the discussion section which shows increased breaks in gmc2 and ecm11 mutants. This work was done independently by Keun Kim, Miki Shinohara and colleagues. The pulse gel electrophoresis result shown in Figure 1D has been re-quantified. The conclusion remains that homeologous and monosomic chromosome V generate more DSBs compared to internally controlled chromosome III. One zip3 map included in PCA (Figure 6C) and hierarchical clustering analysis (Figure S5B) has been deleted because this particular map has not yet been published. This change does not affect the conclusion. An additional supplemental table (S5) has been added to show Spo11-oligo datasets used in this study. Figures and preprint have been reformatted. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/089367v2_fig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@871eaforg.highwire.dtl.DTLVardef@ef7995org.highwire.dtl.DTLVardef@176441org.highwire.dtl.DTLVardef@1b6e772_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Higher DSB levels on homolog-engagement defective chromosomes. (A) Cartoons of wild-type, homeologous, monosomic and trisomic chromosome configurations. Grey lines are S. cerevisiae chromosomes and orange lines are S. pastorianus. The homeologous chrV pair rarely synapses or recombines. The trisomic chromosomes can adopt different synaptic configurations ("II+I", partner switch, and triple synapsis). (B) Representative PFGE Southern blots probed for chrIII and chrV. P, signal from parental-length DNA; W, signal in wells. Asterisk indicates an ectopic recombination product between leu2::hisG (on chrIII) and ho::hisG (on chrIV) in the monosomic strain. The other strains do not form this product because they do not have a hisG insert at ho. (C) Poisson-corrected DSB quantification of PFGE Southern blots. (D) Quantification of time-averaged DSBs on chrV relative to chrIII for wild-type, homeologous and monosomic strains. * p<0.05, unpaired t test. Error bars in C, D are mean {+/-} SD except for the monosomic strain (mean {+/-} range). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/089367v2_fig6.gif" ALT="Figure 6"> View larger version (36K): org.highwire.dtl.DTLVardef@1152edforg.highwire.dtl.DTLVardef@1b853daorg.highwire.dtl.DTLVardef@89392dorg.highwire.dtl.DTLVardef@108d65a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO gmc2{Delta} and ecm11{Delta} mutants share similar homolog-engagement signatures as zip3{Delta}. (A, B) Representative labeling of Spo11-oligo complexes in gmc2{Delta} (A) and ecm11{Delta} (B) mutants and quantification relative to wild-type cultures processed in parallel. Error bars indicate mean {+/-} SD for 3 cultures. Radiolabeled Spo11-oligo complexes are detected by autoradiography (left panel, top) and total Spo11 is detected by anti-Flag western blot (WB; left panel, bottom). The two main labeled species differ in the sizes of oligos (Neale et al. 2005). Most Spo11 protein does not end up making DSBs, so nearly all of the visible western blot signal is from free Spo11 that does not have an oligo attached (Neale et al. 2005). (C) Principal component analysis of 21 wild-type and mutant Spo11-oligo maps. (D) Loss of anticorrelation between chromosome length and DSB density in homolog-engagement-defective mutants. Each point is one chromosome. Correlation coefficients (Pearsons r) are shown. (E) Fold change of Spo11-oligo counts in different chromosomal domains. Tel, within 20 kb of telomeres; Cen, within 10 kb of centromeres; rDNA, from 60 kb leftward to 30 kb rightward of rDNA; Interstitial, all others. Horizontal dashed lines mark values assumed as no change (black) and average change (1.8-fold for zip3{Delta}, cyan; 1.7-fold for ecm11{Delta}, purple). Boxes indicate median and interquartile range; whiskers indicate the most extreme data points that are [&le;] 1.5 times the interquartile range from the box; individual points are outliers C_FIG O_FIG O_LINKSMALLFIG WIDTH=174 HEIGHT=200 SRC="FIGDIR/small/089367v2_figS5.gif" ALT="Figure 5"> View larger version (35K): org.highwire.dtl.DTLVardef@130cbf6org.highwire.dtl.DTLVardef@9ebe8forg.highwire.dtl.DTLVardef@1f0a2b4org.highwire.dtl.DTLVardef@14a0fcf_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplemental Figure S5.C_FLOATNO DSB patterns in gmc2{Delta} and ecm11{Delta} mutants. (A) Meiotic progression showing percentage of cells completing the first divisions (total bi- and tetra-nucleate cells, mean {+/-} SD, 3 cultures each). At least 100 cells were counted at each time point for each culture. (B) Hierarchical clustering analysis using the "Ward D2" method for 21 wild-type and mutant maps. The y-axis represents height of the cluster dendrogram. In the label for each data set, the letters A, B, C and D stand for maps generated by Xiaojing Mu, Neeman Mohibullah, Megan van Overbeek, and Xuan Zhu, respectively, and the numerals distinguish biological replicate maps. (C) Regional variation in response to zip3{Delta} and ecm11{Delta} mutations for chromosome XII. Lines, local regression (loess) based on Spo11-oligo density changes in 5 kb-bins; green circle, centromere; rDNA location is labeled. (D, E) Fold change of Spo11-oligo densities for zip3{Delta} and ecm11{Delta} compared to wild type in pericentric (D) and telomere-proximal (E) regions. Lines, local regression (loess) for data in 5 kb-bins averaged across 32 chromosome arms; dashed line, no change in black and genome average change in cyan (1.8-fold, zip3{Delta}) and purple (1.7-fold, ecm11{Delta}); yellow shading, zones suppressed for DSB formation as previously defined (Pan etal. 2011). C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@15408baorg.highwire.dtl.DTLVardef@9171aorg.highwire.dtl.DTLVardef@cbabfaorg.highwire.dtl.DTLVardef@187d594org.highwire.dtl.DTLVardef@d6eb68_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOSupplemental Table S5.C_FLOATNO O_TABLECAPTIONSpo11-oligo datasets used in this study C_TABLECAPTION C_TBL

genetics↗
bioRxiv2020

The importance of orangutans in small fragments for maintaining metapopulation dynamics

Orangutans (Pongo spp.) occur at low densities and therefore large areas are necessary to sustain viable metapopulations, defined here as sets of conspecific units of individuals linked by dispersal. Historically, orangutans lived in large contiguous areas of intact rainforest, but are now increasingly found in agricultural and other landscapes modified by people. Here we collate evidence of orangutans utilizing isolated forest fragments (< 500 ha) within multiple-use landscapes dominated by oil palm monoculture across Borneo. Orangutan signs (i.e. nests) were evident in 76 fragments surveyed by helicopter, and in 50 of 70 additional fragments surveyed on the ground; on average 63 ha in size. This includes presence of adult resident females with dependent young confirmed in 40% of the fragments assessed by ground survey. Our study revealed some resident females are raising offspring in isolated forest patches within mature oil palm stands. This not only confirms that some forest patches can sustain orangutans, but indicates migratory males are capable of reaching these fragments scattered throughout the multiple-use landscape. Therefore, orangutans that use or live in even small isolated forest patches are an essential part of the overall metapopulation by maintaining gene flow between, and genetic connectivity within, populations distributed across larger multiple-use landscapes. Orangutan survival is commonly thought to be low in small, isolated forest patches, and the customary management strategy is to remove (translocate) these individuals and release them in larger forests. In some cases, translocations may be necessary, i.e. in case of fire or when the animals are in eminent danger of being killed and have no other refuge. However, the small amount of data available indicates that mortality rates during and after translocations are high, while the impacts of removing animals from spatially dispersed metapopulations are unknown. Therefore, we argue the current policy of routine translocation rather than conserving the species within human-modified landscapes could inadvertently decrease critical metapopulation functionality necessary for long-term viability. It is clear that orangutans need natural forest to survive, but our findings show that fragmented agricultural landscapes can also serve as complementary conservation areas in addition to fully protected areas if they are well designed with ecological connections, and if orangutan killing can be prevented. To achieve this, we call for a paradigm shift from the traditional large single forest model to one that emphasizes metapopulation functionality in the fragmented forest - human use matrix characteristic of the Anthropocene. Version 2 (20 May 2020): this manuscript is a non-peer reviewed preprint shared via the BiorXiv server while being considered for publication in a peer-reviewed academic journal. Please refer to the permanent digital object identifier (https://doi.org/10.1101/2020.05.17.100842). Under the Creative Commons license (CC-BY Attribution-Non Commercial-No Derivatives 4.0 International) you are free to share the material as long as the authors are credited, you link to the license, and indicate if any changes have been made. You may not share the work in any way that suggests the licensor endorses you or your use. You cannot change the work in any way or use it commercially.

ecology↗
bioRxiv2020

The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic

Observations made from papers submitted to preprint servers, and the speculation of editors on social media platforms, suggest that women are submitting fewer papers to scholarly journals than are men during the COVID-19 pandemic. Here I examine whether submissions by men and women to six ecology journals (all published by the British Ecological Society) have changed since the start of COVID disruptions. At these six ecology journals there is no evidence of a decline in the proportion of submissions that are authored by women (as either first or submitting author) since the start of the COVID-19 disruptions; the proportion of papers authored by women in the post-COVID period of 2020 has increased relative to the same period in 2019, and is higher than in the period pre-COVID in 2020. There is also no evidence of a change in the geographic pattern of submissions from across the globe.Competing Interest StatementCharles Fox is Executive Editor of Functional Ecology, one of the journals that contributed data for the analyses presented in this paper.View Full Text

scientific communication and education↗
bioRxiv2020

An innovative approach for HLA typing, molecular tumor testing and the validation of tumor exclusive antigens

DisclaimerThis manuscript has been withdrawn by the corresponding author, as it was submitted and made public in bioRxiv without knowledge and the full consent of all the authors listed. The co-authors are therefore not responsible for the contents of this manuscript. For this reason, the submitting author has chosen to withdraw this preprint as a precautionary measure and would like to state that this work should not be cited as a reference. For any related questions that may arise, please contact the corresponding author.Competing Interest StatementThe authors have declared no competing interest.

immunology↗
bioRxiv2020

Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19

ABSTRACTThe COVID-19 pandemic took us ill-prepared and tackling the many challenges it poses in a timely manner requires world-wide collaboration. Our ability to study the SARS-COV-2 virus and its interactions with its human host in molecular terms efficiently and collaboratively becomes indispensable and mission-critical in the race to develop vaccines, drugs, and neutralizing antibodies. There is already a significant corpus of 3D structures related to SARS and MERS coronaviruses, and the rapid generation of new structures demands the use of efficient tools to expedite the sharing of structural analyses and molecular designs and convey them in their native 3D context in sync with sequence data and annotations. We developed iCn3D (pronounced “I see in 3D”) 1 to take full advantage of web technologies and allow scientists of different backgrounds to perform and share sequence-structure analyses over the Internet and engage in collaborations through a simple mechanism of exchanging “lifelong” web links (URLs). This approach solves the very old problem of “sharing of molecular scenes” in a reliable and convenient manner. iCn3D links are sharable over the Internet and make data and entire analyses findable, accessible, and reproducible, with various levels of interoperability. Links and underlying data are FAIR 2 and can be embedded in preprints and papers, bringing a 3D live and interactive dimension to a world of text and static images used in current publications, eliminating at the same time the need for arcane supplemental materials. This paper exemplifies iCn3D capabilities in visualization, analysis, and sharing of COVID-19 related structures, sequence variability, and molecular interactions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗
bioRxiv2020

Dynamics of the COVID -19 Related Publications

BackgroundThis study aims to analyze the dynamics of the published articles and preprints of Covid-19 related literature from different scientific databases and sharing platforms. MethodsThe PubMed, Elsevier, and Research Gate (RG) databases were under consideration in this study over a specific time. Analyses were carried out on the number of publications as (a) function of time (day), (b) journals and (c) authors. Doubling time of the number of publications was analyzed for PubMed "all articles" and Elsevier published articles. Analyzed databases were (1A) PubMed "all articles" (01/12/2019-12/06/2020) (1B) PubMed Review articles (01/12/2019-2/5/2020) and (1C) PubMed Clinical Trials (01/01/2020-30/06/2020) (2) Elsevier all publications (01/12/2019-25/05/2020) (3) RG (Article, Pre Print, Technical Report) (15/04/2020-30/4/2020). FindingsTotal publications in the observation period for PubMed, Elsevier, and RG were 23000, 5898 and 5393 respectively. The average number of publications/day for PubMed, Elsevier and RG were 70.0 {+/-}128.6, 77.6{+/-}125.3 and 255.6{+/-}205.8 respectively. PubMed shows an avalanche in the number of publication around May 10, number of publications jumped from 6.0{+/-}8.4/day to 282.5{+/-}110.3/day. The average doubling time for PubMed, Elsevier, and RG was 10.3{+/-}4 days, 20.6 days, and 2.3{+/-}2.0 days respectively. In PubMed average articles/journal was 5.2{+/-}10.3 and top 20 authors representing 935 articles are of Chinese descent. The average number of publications per author for PubMed, Elsevier, and RG was 1.2{+/-}1.4, 1.3{+/-}0.9, and 1.1{+/-}0.4 respectively. Subgroup analysis, PubMed review articles mean and median review time for each article were <0|17{+/-}17|77> and 13.9 days respectively; and reducing at a rate of-0.21 days (count)/day. InterpretationAlthough the disease has been known for around 6 months, the number of publications related to the Covid-19 until now is huge and growing very fast with time. It is essential to rationalize the publications scientifically by the researchers, authors, reviewers, and publishing houses. FundingNone

scientific communication and education↗
bioRxiv2020

The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR

On 22 January 2020, the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), created the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access SARS-CoV-2 information resource. 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by our in-house automated pipeline. Of particular note, 2019nCoVR performs systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. It also generates visualization of the spatiotemporal change for each variant and yields historical viral haplotype network maps for the course of the outbreak from all complete and high-quality genomes. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on COVID-19 (Coronavirus Disease 2019), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB-NGDC, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with National Center for Biotechnology Information. Collectively, all SARS-CoV-2 genome sequences, variants, haplotypes and literature are updated daily to provide timely information, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.

genomics↗
bioRxiv2020

Does the Inertia of a Cell Depend Upon its Information-Content?

A time dilation factor is derived from information entropy via the holographic principle. By imagining the embryonic cell as a hologram, time dilation during embryogenesis is predicted from the entropy of active genetic information and shown to be consistent with observed lengths of cell duration. The connection between entropy and cell duration as well as the corollary of increase in cellular mass with the reduction in information entropy are discussed. This preprint is the second in a series exploring the value of Developmental Spacetime as a framework for falsifiable predictions about the universe.

developmental biology↗
bioRxiv2020

EEG-based decoding and recognition of imagined music

The authors have withdrawn their manuscript because they discovered an error in the analysis code after publication of the preprint, which turns out to have a major impact on the main results in the paper. The results on the imagination data become non-significant after correcting for the mistake. Significant results on the perception data are preserved, although the classification results are worse than what is reported. Therefore, the authors do not wish this work to be cited as a reference. If you have any questions, please contact the last author.

neuroscience↗
bioRxiv2020

Role of 5-HT2C receptors in zebrafish alarm reactions and post-exposure behavior

Serotonin (5-HT) receptors have been implicated in responses to aversive stimuli in mammals and fish, but its precise role is still unknown. Moreover, since at least seven families of 5-HT receptors exist in vertebrates, the role of specific receptors is still debated. Aversive stimuli can be classified as indicators of proximal, distal, or potential threat, initiating responses that are appropriate for each of these threat levels. Responses to potential threat usually involve cautious exploration and increased alertness, while responses to distal and proximal threat involve a fight-flight-freeze reaction. We exposed adult zebrafish to a conspecific alarm substance (CAS) and observed behavior during (distal threat) and after (potential threat) exposure, and treated with the 5-HT2C receptor agonists MK-212 or WAY-161503 or with the antagonist RS-102221. The agonists blocked CAS-elicited defensive behavior (distal threat), but not post-exposure increases in defensive behavior (potential threat), suggesting inhibition of responses to distal threat. MK-212 blocked changes in freezing elicited by acute restraint stress, a model of proximal threat, while RS-102221 blocked changes in geotaxis elicited this stressor. We also found that RS-102221, a 5-HT2C receptor antagonist, produced small effect on behavior during and after exposure to CAS. Preprint: https://www.biorxiv.org/content/10.1101/2020.10.04.324202; Data and scripts: https://github.com/lanec-unifesspa/5-HT-CAS/tree/master/data/5HT2C

neuroscience↗
bioRxiv2020

An improved comprehensive strategy for deep and quantitative N-glycomics based on optimization of sample preparation, isotope-based data quality control and quantification, new N-glycan libraries and new algorithms

Withdrawal statement"The authors have withdrawn their manuscript because the authors need to re-organize the data and writing, meanwhile more experimental evidence from human cellular N-glycome will be added to support their viewpoints. In this preprint, only one human cell line, Acute Promyelocytic Leukemia (APL) cells, was deeply investigated to show the N-glycome landscape. To provide the shared features of human N-glycome, more human cells should be investigated. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author."

biochemistry↗
bioRxiv2020

Human temporal voice areas are sensitive to chimpanzee vocalizations

Withdrawal StatementThe authors have withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2025/677258. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. The correct preprint can be found at doi: 10.1101/2025.09.19.677258

neuroscience↗
bioRxiv2020

Developmental regulation of mitotic chromosome formation revealed by condensin reporter mice

Withdrawal Note: The authors have withdrawn their manuscript due to the discovery of artifacts that call into question key findings from the study. Both artifacts originate from cell-type differences that arose during sample processing, creating the impression that non-SMC subunits of condensin proteins were present at substantially higher levels in thymic T cells compared to bone marrow B cells or erythroblast cells. Based on data collected since the preprint was submitted, we no longer believe this to be true. The experimental artifacts do not affect the data contributed by the Papadopoulos laboratory (Figure 4). The authors wish to make it clear that all data and experimental protocols in the original manuscript were accurately reported, and that the experimental artifacts which affect data interpretation were discovered during internal review, independently of peer review, and are being reported at the authors own instigation. They do not, to our knowledge, affect the interpretation of data from any other published work. Due to the issues outlined above, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

cell biology↗